| summary_results |
1 |
- WGCA_analysis_result/RGI_heatmap
- WGCA_analysis_result/virulence_summary.tsv
- WGCA_analysis_result/plasmid_summary.tsv
- WGCA_analysis_result/RGI_heatmap-4.png
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| summarize_plasmid_prediction |
1 |
- plasmid_prediction/summary.tsv
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|
- abricate =0.8.13
- perl-list-moreutils
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| abricate --summary {input} > {output}
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| summarize_virulence |
1 |
- virulence_genes/summary.tsv
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|
- abricate =0.8.13
- perl-list-moreutils
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| abricate --summary {input} > {output}
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| generate_resistome_heatmap |
1 |
- resistome_summary/RGI_heatmap
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|
|
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| genomic_island_prediction |
4 |
- genomic_islands/C7_GI.gff3
- genomic_islands/D2_GI.gff3
- genomic_islands/B9_GI.gff3
- genomic_islands/DMW1-1_GI.gff3
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|
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| islandpath {input} {output}
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| plasmid_prediction |
4 |
- plasmid_prediction/C7.tsv
- plasmid_prediction/D2.tsv
- plasmid_prediction/B9.tsv
- plasmid_prediction/DMW1-1.tsv
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|
- abricate =0.8.13
- perl-list-moreutils
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| abricate --minid=60 --mincov=90 --db=plasmidfinder {input} > {output}
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| virulence_identification |
4 |
- virulence_genes/C7.tsv
- virulence_genes/D2.tsv
- virulence_genes/B9.tsv
- virulence_genes/DMW1-1.tsv
|
|
- abricate =0.8.13
- perl-list-moreutils
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| abricate --minid=90 --mincov=60 --db=vfdb {input} > {output}
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| resistome_prediction |
4 |
- resistome_prediction/C7
- resistome_prediction/D2
- resistome_prediction/B9
- resistome_prediction/DMW1-1
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|
|
| docker run -v $PWD:/data -t quay.io/biocontainers/rgi:4.2.2--py35ha92aebf_1 rgi main -i data/{input} -o data/resistome_prediction/{wildcards.sample} -t contig --clean --debug > {output.log}
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| genome_annotation |
4 |
- genome_annotation/C7.gbk
- genome_annotation/D2.gbk
- genome_annotation/B9.gbk
- genome_annotation/DMW1-1.gbk
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|
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| prokka --force --outdir genome_annotation/ --usegenus --Genus Enterococcus --prefix {wildcards.sample} {input}
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